Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004474.1 Hibiscus syriacus cultivar Beakdansim tig00009863_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 80840
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9808 original size:27 final size:27
Alignment explanation
Indices: 9773--9828 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
9763 GGTTATGAAT
9773 CTGCTGCTCCCGCATACGTTCCAGCTG
1 CTGCTGCTCCCGCATACGTTCCAGCTG
9800 CTGCTGCTCCCGCATACGTTCCAGCTG
1 CTGCTGCTCCCGCATACGTTCCAGCTG
9827 CT
1 CT
9829 CCAGCTGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.11, C:0.41, G:0.21, T:0.27
Consensus pattern (27 bp):
CTGCTGCTCCCGCATACGTTCCAGCTG
Found at i:9839 original size:36 final size:36
Alignment explanation
Indices: 9792--9884 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
9782 CCGCATACGT
9792 TCCAGCTGCTGCTGCTCCCGCATACGTTCCAGCTGC
1 TCCAGCTGCTGCTGCTCCCGCATACGTTCCAGCTGC
* * *
9828 TCCAGCTGCTGCTGTTCCCGCATACGTTCCCGCTGT
1 TCCAGCTGCTGCTGCTCCCGCATACGTTCCAGCTGC
*
9864 TCCAGCTGCTGCTGCTGCCGC
1 TCCAGCTGCTGCTGCTCCCGC
9885 CGCTGAAGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.09, C:0.41, G:0.24, T:0.27
Consensus pattern (36 bp):
TCCAGCTGCTGCTGCTCCCGCATACGTTCCAGCTGC
Found at i:9902 original size:27 final size:27
Alignment explanation
Indices: 9872--9952 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
9862 GTTCCAGCTG
* *
9872 CTGCTGCTGCCGCCGCTGAAGTTCCAA
1 CTGCAGCTGCCGCCGCTCAAGTTCCAA
* **
9899 CTGCAGCTGCTGTTGCTCAAGTTCCAA
1 CTGCAGCTGCCGCCGCTCAAGTTCCAA
* * * **
9926 CTGCCGATGCTGTTGCTCAAGTTCCAA
1 CTGCAGCTGCCGCCGCTCAAGTTCCAA
9953 TTGCCGATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.17, C:0.32, G:0.23, T:0.27
Consensus pattern (27 bp):
CTGCAGCTGCCGCCGCTCAAGTTCCAA
Found at i:9957 original size:27 final size:27
Alignment explanation
Indices: 9890--9966 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
9880 GCCGCCGCTG
* *
9890 AAGTTCCAACTGCAGCTGCTGTTGCTC
1 AAGTTCCAACTGCCGATGCTGTTGCTC
9917 AAGTTCCAACTGCCGATGCTGTTGCTC
1 AAGTTCCAACTGCCGATGCTGTTGCTC
*
9944 AAGTTCCAATTGCCGATGCTGTT
1 AAGTTCCAACTGCCGATGCTGTT
9967 CAAATTGAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.31
Consensus pattern (27 bp):
AAGTTCCAACTGCCGATGCTGTTGCTC
Found at i:18318 original size:30 final size:30
Alignment explanation
Indices: 18282--18501 Score: 201
Period size: 30 Copynumber: 7.3 Consensus size: 30
18272 TGGTGACGAA
** *
18282 GCTGCTGCTGTTGCCGTTGAAGTTCCAACT
1 GCTGCTGCTGCCGCCGCTGAAGTTCCAACT
* *
18312 GCTGCTGCTGCCGCCGTTCAAGTTCCAACT
1 GCTGCTGCTGCCGCCGCTGAAGTTCCAACT
* * ** * *
18342 GCTTCTGGTGCTTCTGCTGAAATTCCAACT
1 GCTGCTGCTGCCGCCGCTGAAGTTCCAACT
* * *
18372 GCTGCTGGTGTCGCCGCTGAAGTTCCAGCT
1 GCTGCTGCTGCCGCCGCTGAAGTTCCAACT
**
18402 GCTGCTGCTGCCGCAACTGAAGTTCCAACT
1 GCTGCTGCTGCCGCCGCTGAAGTTCCAACT
* * *
18432 GTTGCTGCTGCAGCAGCTGAA-TCTCCAACT
1 GCTGCTGCTGCCGCCGCTGAAGT-TCCAACT
* *
18462 GCTGCTGCTGCAGCAGCTGAA-TCTCCAACT
1 GCTGCTGCTGCCGCCGCTGAAGT-TCCAACT
* *
18492 GTTGTTGCTG
1 GCTGCTGCTG
18502 TCGTTGCTGT
Statistics
Matches: 160, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
29 1 0.01
30 159 0.99
ACGTcount: A:0.15, C:0.30, G:0.25, T:0.29
Consensus pattern (30 bp):
GCTGCTGCTGCCGCCGCTGAAGTTCCAACT
Found at i:18396 original size:90 final size:90
Alignment explanation
Indices: 18282--18501 Score: 241
Period size: 90 Copynumber: 2.4 Consensus size: 90
18272 TGGTGACGAA
* * ***
18282 GCTGCTGCTGTTGCCGTTGAAGTTCCAACTGCTGCTGCTGCCGCCGTTCAAGTTCCAACTGCTT-
1 GCTGCTGCTGTCGCCGCTGAAGTTCCAACTGCTGCTGCTGCCGCAACTCAAGTTCCAACTG-TTG
* ** *
18346 CTGGTGCTTCTGCTGAAAT-TCCAACT
65 CTGCTGCAGCAGCTG-AATCTCCAACT
* * *
18372 GCTGCTGGTGTCGCCGCTGAAGTTCCAGCTGCTGCTGCTGCCGCAACTGAAGTTCCAACTGTTGC
1 GCTGCTGCTGTCGCCGCTGAAGTTCCAACTGCTGCTGCTGCCGCAACTCAAGTTCCAACTGTTGC
18437 TGCTGCAGCAGCTGAATCTCCAACT
66 TGCTGCAGCAGCTGAATCTCCAACT
* * *
18462 GCTGCTGCTG-CAGCAGCTGAA-TCTCCAACTGTTGTTGCTG
1 GCTGCTGCTGTC-GCCGCTGAAGT-TCCAACTGCTGCTGCTG
18502 TCGTTGCTGT
Statistics
Matches: 109, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
89 7 0.06
90 102 0.94
ACGTcount: A:0.15, C:0.30, G:0.25, T:0.29
Consensus pattern (90 bp):
GCTGCTGCTGTCGCCGCTGAAGTTCCAACTGCTGCTGCTGCCGCAACTCAAGTTCCAACTGTTGC
TGCTGCAGCAGCTGAATCTCCAACT
Found at i:23562 original size:21 final size:22
Alignment explanation
Indices: 23538--23589 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
23528 ATTTAGATCA
*
23538 TTTAA-TTTAAAATTTAAATTT
1 TTTAATTTTAAAATTAAAATTT
*
23559 TTTAATTTTATAATTAAAA-TT
1 TTTAATTTTAAAATTAAAATTT
*
23580 TTAAATTTTA
1 TTTAATTTTA
23590 TTCATTTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAATTTTAAAATTAAAATTT
Found at i:23597 original size:29 final size:26
Alignment explanation
Indices: 23535--23597 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 26
23525 CACATTTAGA
*
23535 TCATTTAATTTAAAATTTAAATTTTT
1 TCATTTAAATTAAAATTTAAATTTTT
*
23561 TAATTTTATAATTAAAATTTTAAATTTTAT
1 TCA-TTTA-AATTAAAA-TTTAAATTTT-T
23591 TCATTTA
1 TCATTTA
23598 GATGATTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.07
27 4 0.13
28 7 0.23
29 14 0.47
30 3 0.10
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (26 bp):
TCATTTAAATTAAAATTTAAATTTTT
Found at i:29331 original size:21 final size:21
Alignment explanation
Indices: 29305--29444 Score: 185
Period size: 21 Copynumber: 6.7 Consensus size: 21
29295 GTTTCCAGAT
*
29305 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
29326 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
29347 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
** *
29368 TCGCAATGCGAA-TATATA-AA
1 TCGCAATGCGAACT-TCGACTA
*
29388 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
29409 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTCGACTA
29430 TCGCAATGCGAACTT
1 TCGCAATGCGAACTT
29445 GCGAACTTGG
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
20 16 0.15
21 89 0.85
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:29391 original size:62 final size:62
Alignment explanation
Indices: 29325--29441 Score: 207
Period size: 62 Copynumber: 1.9 Consensus size: 62
29315 AACTTCGACT
*
29325 ATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATATAA
1 ATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAATGCGAATATATAA
* *
29387 ATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTTGACTATCGCAATGCGAA
1 ATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAATGCGAA
29442 CTTGCGAACT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (62 bp):
ATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAATGCGAATATATAA
Found at i:30169 original size:6 final size:6
Alignment explanation
Indices: 30158--30194 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
30148 TCGCCTCGCC
30158 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
30195 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:33632 original size:21 final size:20
Alignment explanation
Indices: 33593--33630 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
33583 AGAATGTCCA
33593 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
33613 GGGGGTATCGATTCCCCC
1 GGGGGTATCGATTCCCCC
33631 CTAAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:33994 original size:14 final size:15
Alignment explanation
Indices: 33977--34005 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33967 TACATGATAT
33977 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
33991 GCATAAAACATAAGA
1 GCATAAAACATAAGA
34006 TATATGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:34299 original size:15 final size:15
Alignment explanation
Indices: 34281--34330 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
34271 CGAGGGTATT
34281 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
34296 GTAGTCGTTCGGGAC
1 GTAGTCCTTCGGGAC
34311 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
34326 GTAGT
1 GTAGT
34331 GGTCCTACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.36, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:40031 original size:14 final size:15
Alignment explanation
Indices: 40014--40042 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40004 TACATGATAT
40014 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
40028 GCATAAAACATAAGA
1 GCATAAAACATAAGA
40043 TATATGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:40336 original size:15 final size:15
Alignment explanation
Indices: 40318--40352 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40308 CGAGGGTATT
*
40318 GTAGTCGTTCGGGAC
1 GTAGTCCTTCGGGAC
40333 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
40348 GTAGT
1 GTAGT
40353 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.20, G:0.37, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:43902 original size:19 final size:18
Alignment explanation
Indices: 43866--43905 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
43856 AAAACACAAT
*
43866 AATTAGAAATTTTTGAAA
1 AATTAAAAATTTTTGAAA
*
43884 AATTAAAAATTTTTGGAA
1 AATTAAAAATTTTTGAAA
43902 AATT
1 AATT
43906 CTTGTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (18 bp):
AATTAAAAATTTTTGAAA
Found at i:44342 original size:20 final size:21
Alignment explanation
Indices: 44289--44350 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
44279 ATTCCCCTGT
44289 TGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGAATCGGTT-CCC-TCAA
*
44312 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGAATCGGTTCCCTCAA
* *
44332 TGGGGGGATCGATTCCCTC
1 TGGGGGAATCGGTTCCCTC
44351 TGCACAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (21 bp):
TGGGGGAATCGGTTCCCTCAA
Found at i:48197 original size:22 final size:21
Alignment explanation
Indices: 48155--48194 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48145 GAGTTTGTTT
*
48155 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
48176 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
48195 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:50056 original size:21 final size:21
Alignment explanation
Indices: 50030--50084 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
50020 GGAGCGTGGG
50030 GGGAATCGGTTCCTCCTTATA
1 GGGAATCGGTTCCTCCTTATA
50051 GGGAATCGGTTCCTCCTTATA
1 GGGAATCGGTTCCTCCTTATA
50072 GGGAATCGGTTCC
1 GGGAATCGGTTCC
50085 CTAAGTGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
GGGAATCGGTTCCTCCTTATA
Found at i:50965 original size:33 final size:34
Alignment explanation
Indices: 50927--51010 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
50917 CGATTATATA
50927 TATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
50960 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
50994 TATATATAAAATATTTT
1 TATATATATAATATTTT
51011 CGGGTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 20 0.41
34 29 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:52481 original size:14 final size:15
Alignment explanation
Indices: 52439--52481 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 15
52429 TGAAATCGAT
52439 TTTTTTCGGTTCGGG
1 TTTTTTCGGTTCGGG
52454 TTTTTTAACGGTTCGGG
1 TTTTTT--CGGTTCGGG
52471 -TTTTTCGGTTC
1 TTTTTTCGGTTC
52482 TGTTCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.23
15 6 0.23
16 5 0.19
17 9 0.35
ACGTcount: A:0.05, C:0.14, G:0.28, T:0.53
Consensus pattern (15 bp):
TTTTTTCGGTTCGGG
Found at i:53253 original size:41 final size:42
Alignment explanation
Indices: 53207--53298 Score: 100
Period size: 41 Copynumber: 2.2 Consensus size: 42
53197 AATTTTCTAA
* *
53207 TTTATATAAAAATTAAATATTTTATAATTCA-AAAA-AAAAAG
1 TTTATATAAAAATTAAATAATATATAATT-ATAAAATAAAAAG
* * *
53248 TTTATA-ATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 TTTATATA-AAAATTAAATAATATATAATTATAAAATAAAAAG
53290 TTTATATAA
1 TTTATATAA
53299 TTTTTTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
40 2 0.05
41 27 0.66
42 11 0.27
43 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (42 bp):
TTTATATAAAAATTAAATAATATATAATTATAAAATAAAAAG
Found at i:53481 original size:186 final size:187
Alignment explanation
Indices: 53209--53601 Score: 648
Period size: 186 Copynumber: 2.1 Consensus size: 187
53199 TTTTCTAATT
* * *
53209 TATATAA-AAATTAAATATTTTATAATTCAAAAAAAAAAGTTTATAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTATAATTCAAAAAAAAAAGTTTACAATTAATTTAAATAATATAT
* *
53273 AATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAATTT
66 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTT
* *
53338 ATTGGATCTTAAATTATTAATTGGGTTTTAAAAGGTTT-GGACTGAGTCCATATGTTA
131 ATTGAATCTTAAATTATTAATTGGATTTTAAAAGGTTTGGGA-TGAGTCCATATGTTA
* * *
53395 TATATAATATATTTAATATTTTTTAATTCAGAAAAACAA-TTTACAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTATAATTCAAAAAAAAAAGTTTACAATTAATTTAAATAATATAT
*
53459 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTATGTTTAAAAGTT
66 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTT
*
53524 ATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGATGAGTCCATATGTTA
131 ATTGAATCTTAAATTATTAATTGGATTTTAAAAGGTTTGGGATGAGTCCATATGTTA
53581 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
53602 ACAATTTTAT
Statistics
Matches: 193, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
186 164 0.85
187 29 0.15
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (187 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAAAAAGTTTACAATTAATTTAAATAATATAT
AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTT
ATTGAATCTTAAATTATTAATTGGATTTTAAAAGGTTTGGGATGAGTCCATATGTTA
Found at i:57208 original size:79 final size:80
Alignment explanation
Indices: 57018--57278 Score: 341
Period size: 79 Copynumber: 3.3 Consensus size: 80
57008 GGGTCTATGG
* * *
57018 GCCTACTCAAGGATATCCTTAGATCCGTAAGGTTACCTTAAGCACACAACAAAAAGG-AACCAAC
1 GCCTACCCAAGGATATCCTTAGATCTGTAGGGTTACCTTAAGCACACAAC--AAAGGAAACCAAC
* * *
57082 CTAAAGATATACGTTGA
64 CTAAGGATATGCCTTGA
* * * *
57099 GTCTACCCAAGGATATCTTTATAT-TCGTAGGGTTACCTTAAGCACACAGCAAAGGAAACCAACC
1 GCCTACCCAAGGATATCCTTAGATCT-GTAGGGTTACCTTAAGCACACAACAAAGGAAACCAACC
57163 TAAGGATATGCCTT-A
65 TAAGGATATGCCTTGA
* *
57178 GCCTACCCAAGGACATCCTTAGATCTGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCT
1 GCCTACCCAAGGATATCCTTAGATCTGTAGGGTTACCTTAAGCACACAACAAAGGAAACCAACCT
*
57243 AAGGATATGCCTTGG
66 AAGGATATGCCTTGA
*
57258 GCCTACCC-ATGATATCCTTAG
1 GCCTACCCAAGGATATCCTTAG
57279 GTCCTTAAGG
Statistics
Matches: 157, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
79 87 0.55
80 28 0.18
81 42 0.27
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (80 bp):
GCCTACCCAAGGATATCCTTAGATCTGTAGGGTTACCTTAAGCACACAACAAAGGAAACCAACCT
AAGGATATGCCTTGA
Found at i:60701 original size:6 final size:6
Alignment explanation
Indices: 60690--60722 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
60680 ACAGCTTCAT
60690 TTTTTC TTTTTC TTTTT- TTTTTC -TTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
60723 TTTACAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTC
Found at i:60711 original size:17 final size:16
Alignment explanation
Indices: 60689--60725 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 16
60679 CACAGCTTCA
60689 TTTTTTCTTTTTCTTTT
1 TTTTTTC-TTTTCTTTT
60706 TTTTTTCTTTTCTTTT
1 TTTTTTCTTTTCTTTT
60722 TTTT
1 TTTT
60726 ACAAAGTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTTCTTTTCTTTT
Found at i:65730 original size:17 final size:17
Alignment explanation
Indices: 65708--65748 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
65698 CTGCTGCCGA
65708 GCTGGTTGATGAGCAGT
1 GCTGGTTGATGAGCAGT
65725 GCTGGTTGATGAGCAGT
1 GCTGGTTGATGAGCAGT
65742 GCTGGTT
1 GCTGGTT
65749 CCTTGATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.15, C:0.12, G:0.41, T:0.32
Consensus pattern (17 bp):
GCTGGTTGATGAGCAGT
Found at i:71881 original size:276 final size:274
Alignment explanation
Indices: 71367--71917 Score: 716
Period size: 276 Copynumber: 2.0 Consensus size: 274
71357 AGTCACTGAT
* *
71367 CTCTAGCTTGTGGAGTTTCTTGCAGCCATTCAACATGTAGTGCATTCCTTTGTCGTCGTCGGCAA
1 CTCTAGCTTGAGGAGTTTCTTGCAGCCATTCAACATGTAGAGCATTCCTTTGTCGTCGTCGGCAA
* * * *
71432 AAGCGATGGACGACATTTCGAGCAGCTCGGCATATATTCCTATGTAAAGAAAAACCTGATCGGTC
66 AAGCGATGGACAACATTTCGAGCAGCTCAGCATACATTCCAATGTAAAGAAAAACCTGATCGGTC
** * * *
71497 CAAAGGCTGGAGAGTGATAACCTCTTGCGTCACTTGAATGACTGAGCAATTGCCCTAAAACCTTC
131 CAAAGGCCAGAGAGTGATAACCTC-TGAGTCACTTGAATGACTGAACAATCGCCCTAAAACCTTC
* * *
71562 ATCTAATGGCTGATTGGTTGCAGGGTCAGGTTTTTCAGGGGTCCTCAATCCACAATTTGATCAGT
195 ATCTAATGGCTGATTGGTTACAGGGTCAAGTTTTTCAGGGGTCCTCAATCCACAATTTCATCAGT
71627 AAAAAAATATATATTC
260 AAAAAAATATA-ATTC
*
71643 CTCTAGCTTGCAGG-GTTTCTT-CTAGCCATTCAACATGTAGAGCATTCCTTTGTCGTTGTCGGC
1 CTCTAGCTTG-AGGAGTTTCTTGC-AGCCATTCAACATGTAGAGCATTCCTTTGTCGTCGTC-G-
** *
71706 AGCAAAAGCGATGGACAACATTTCGAGTTGTTCAGCATACATTCCAATGTAAAGAAAAACCTGAT
62 -GCAAAAGCGATGGACAACATTTCGAGCAGCTCAGCATACATTCCAATGTAAAGAAAAACCTGAT
* * * * * * *
71771 TGGT-CATAGCGCCAGAGATTGATAACCTC-GAGTCGCTTGCATGATTGAACAATCGCCCTAATA
126 CGGTCCAAAG-GCCAGAGAGTGATAACCTCTGAGTCACTTGAATGACTGAACAATCGCCCTAAAA
* * * **
71834 CCTTCATCTAATGGCTGATTGGTTATATGGTCAAGTTTTTC-GGGGTCCTCGATTGACAATTTCA
190 CCTTCATCTAATGGCTGATTGGTTACAGGGTCAAGTTTTTCAGGGGTCCTCAATCCACAATTTCA
*
71898 TCATTAAAAAAATATAATTC
255 TCAGTAAAAAAATATAATTC
71918 TAAGATTTTA
Statistics
Matches: 238, Mismatches: 31, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
275 5 0.02
276 86 0.36
277 67 0.28
278 4 0.02
279 76 0.32
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (274 bp):
CTCTAGCTTGAGGAGTTTCTTGCAGCCATTCAACATGTAGAGCATTCCTTTGTCGTCGTCGGCAA
AAGCGATGGACAACATTTCGAGCAGCTCAGCATACATTCCAATGTAAAGAAAAACCTGATCGGTC
CAAAGGCCAGAGAGTGATAACCTCTGAGTCACTTGAATGACTGAACAATCGCCCTAAAACCTTCA
TCTAATGGCTGATTGGTTACAGGGTCAAGTTTTTCAGGGGTCCTCAATCCACAATTTCATCAGTA
AAAAAATATAATTC
Found at i:74038 original size:39 final size:39
Alignment explanation
Indices: 73981--74057 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
73971 GGCTTCCAAG
73981 TGAGTGCATTCTACGGTTGCATTTGCATTTTCTTTTATA
1 TGAGTGCATTCTACGGTTGCATTTGCATTTTCTTTTATA
* *
74020 TGAGTGCATTCTATGGTTGTATTTGCATTTTCTTTTAT
1 TGAGTGCATTCTACGGTTGCATTTGCATTTTCTTTTAT
74058 GAGTGATAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.17, C:0.13, G:0.18, T:0.52
Consensus pattern (39 bp):
TGAGTGCATTCTACGGTTGCATTTGCATTTTCTTTTATA
Found at i:76308 original size:25 final size:25
Alignment explanation
Indices: 76280--76333 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
76270 AAATGTATTT
76280 CTTAATTTATGTATGGGTTCAACGG
1 CTTAATTTATGTATGGGTTCAACGG
76305 CTTAATTTATGTATGGGTTCAACGG
1 CTTAATTTATGTATGGGTTCAACGG
76330 -TTAA
1 CTTAA
76334 ACTGATTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (25 bp):
CTTAATTTATGTATGGGTTCAACGG
Found at i:77029 original size:22 final size:20
Alignment explanation
Indices: 77004--77047 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
76994 TCCCTTTATT
*
77004 ATGCTCAACTATTTTAGATTTA
1 ATGCTCAA-TATTTCA-ATTTA
*
77026 ATGCTCTATATTTCAATTTA
1 ATGCTCAATATTTCAATTTA
77046 AT
1 AT
77048 AATTTAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.48
Consensus pattern (20 bp):
ATGCTCAATATTTCAATTTA
Found at i:79647 original size:21 final size:21
Alignment explanation
Indices: 79595--79649 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
79585 ATCAGTTCCC
*
79595 AGAATCGCAACGCGATTATAA
1 AGAATCGCAATGCGATTATAA
79616 AGAATCGCAATGCGATTATAA
1 AGAATCGCAATGCGATTATAA
79637 AGAATCGCAATGC
1 AGAATCGCAATGC
79650 AATAGTACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAATCGCAATGCGATTATAA
Found at i:79693 original size:21 final size:21
Alignment explanation
Indices: 79594--79693 Score: 96
Period size: 21 Copynumber: 4.8 Consensus size: 21
79584 AATCAGTTCC
*
79594 CAGAATCGCAACGCGATTATA
1 CAGAATCGCAATGCGATTATA
*
79615 AAGAATCGCAATGCGATTATA
1 CAGAATCGCAATGCGATTATA
* *
79636 AAGAATCGCAATGC-AATAGTA
1 CAGAATCGCAATGCGATTA-TA
* * *
79657 CA-AATTCGCATTGCGATTTTC
1 CAGAA-TCGCAATGCGATTATA
*
79678 CAGAATCGCAACGCGA
1 CAGAATCGCAATGCGA
79694 ATATGTAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.08
21 56 0.86
22 4 0.06
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (21 bp):
CAGAATCGCAATGCGATTATA
Found at i:79706 original size:20 final size:20
Alignment explanation
Indices: 79681--79729 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
79671 GATTTTCCAG
* *
79681 AATCGCAACGCGAATATGTA
1 AATCGCAACGCGAACATATA
79701 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
79721 AATCGCAAC
1 AATCGCAAC
79730 ACGATTCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Done.